相关论文: A combinatorial framework for RNA tertiary interac…
We multiply two $n \times n$ matrices $S,T$ over semirings in the Congested Clique model, where $n$ fully connected nodes communicate synchronously using $O(\log n)$-bit messages, within $O(nz(S)^{1/3} nz(T)^{1/3}/n + 1)$ rounds of…
Let $\Gamma_n$ be the complete undirected Cayley graph of the odd cyclic group $Z_n$. Connected graphs whose vertices are rainbow tetrahedra in $\Gamma_n$ are studied, with any two such vertices adjacent if and only if they share (as…
For some theories where the degrees of freedom are tensors of rank $3$ or higher, there exist solvable large $N$ limits dominated by the melonic diagrams. Simple examples are provided by models containing one rank-$3$ tensor in the…
We study 3-plane drawings, that is, drawings of graphs in which every edge has at most three crossings. We show how the recently developed Density Formula for topological drawings of graphs (KKKRSU GD 2024) can be used to count the…
Periodic networks serve as models for the structural organisation of biological and chemical crystalline systems. Single or multiple networks can have different configurations in space, where entanglement may arise due to the way the…
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We report on the ground state phase diagram of interacting Rydberg atoms in the unfrustrated square lattice array. Using new tensor network algorithms, we scale to large systems in two dimensions while including all long-range interactions,…
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
Self-consistent Green's function theory has recently been extended to the basic formalism needed to account for three-body interactions [A. Carbone, A. Cipollone, C. Barbieri, A. Rios, and A. Polls, (Phys. Rev. C 88, 054326 (2013))]. The…
Summary: Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA),…
New explicit procedures for passing among triplane diagrams, braid movies, and braid charts for knotted surfaces in $\mathbb{R}^4$ are presented. To this end, rainbow diagrams, which lie between braid charts and triplanes, are introduced.…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
We study the enumeration of alternating links and tangles, considered up to topological (flype) equivalences. A weight $n$ is given to each connected component, and in particular the limit $n\to 0$ yields information about (alternating)…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
By considering a class of diagrams which has been overlooked also in the most recent literature on three-body forces, we extract a new contribution to the three-nucleon interaction which specifically acts on the triplet odd states of the…
Many enumeration problems in combinatorics, including such fundamental questions as the number of regular graphs, can be expressed as high-dimensional complex integrals. Motivated by the need for a systematic study of the asymptotic…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
Using the sum-rules, the sum-over-states expression for the diagonal term of first hyperpolarizability can be expressed as the sum of three-state interaction terms. We study the behavior of a generic three-state term to show that is…